Dan, any idea when the next dist release is scheduled? We need to upgrade our wur instance seriously and from then keep up the pace, but it would be a pity if we upgrade and extensively test it now, while the new release is out a few days later. The latest is from November 18th right?! Thanks Alex ________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Daniel Blankenberg [dan@bx.psu.edu] Verzonden: dinsdag 17 januari 2012 15:09 Aan: igv-help@googlegroups.com CC: galaxy-dev@lists.bx.psu.edu; jrobinso@broadinstitute.org Onderwerp: Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a Galaxy visualizer Hi Ming,
From Galaxy, you can currently view BAM and VCF (VCF is available in -central, but will be in the next -dist release) files within IGV. To do this on a local set up, you will need to have your Galaxy instance behind a proxy (e.g. nginx or apache); this enables byte-range requests. In the datatypes_conf.xml file, make sure that '<display file="igv/bam.xml" />' and '<display file="igv/vcf.xml" />' are not commented out. Within Galaxy, your BAM or VCF file should have the dbkey set to a build that is configured to be viewable at IGV (see tool-data/shared/igv/igv_build_sites.txt).
Please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Jan 14, 2012, at 10:09 PM, bt.microzhang@gmail.com<mailto:bt.microzhang@gmail.com> wrote: Hi Guys, I am glad to hear form Jim Robinson that exists some code could wrap IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant and wanted to integrate IGV as a visualizer. I'm looking forward your reply. Regards, Ming ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/